GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Pantoea rwandensis LMG 26275

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_084934993.1 HA51_RS13475 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_002095475.1:WP_084934993.1
          Length = 500

 Score =  140 bits (354), Expect = 4e-38
 Identities = 79/228 (34%), Positives = 132/228 (57%), Gaps = 14/228 (6%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL++R +SKRFG ++AL  V +T++ G+I+ L G NGAGK+T  N+I G+ +PD+G   L
Sbjct: 4   LLELRGISKRFGAVKALQEVDLTLQAGEIHALAGENGAGKSTLMNIIDGILRPDSGEIWL 63

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
           DGKP +  +P E  + GI    Q I L  ++++ EN+ +    R      G +  HK   
Sbjct: 64  DGKPVTIRSPREAQQLGIGLVHQEIALCPDISIYENIWMAHQQR------GLLLPHK--- 114

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
               A+RE++Q++++ +     +K+    LS   Q+ +EIA+AL  D +LL LDEP A +
Sbjct: 115 ----ALRERAQQVMNRLAPIPVSKKVG-ELSLSQQQLVEIAKALTLDCRLLILDEPTAAL 169

Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPI 232
              E   L  ++ +++ +G T++ I H +  +  LC  IT+L  G+ +
Sbjct: 170 TEPEAQTLFSIVRQLRDQGMTVVYISHRMAEIFALCQHITILRDGRTV 217



 Score = 65.5 bits (158), Expect = 2e-15
 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 31/237 (13%)

Query: 5   LLKIRDVS--KRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62
           LL++R++S  KRF      + +   +  G+I G+ G  GAG++     I  L     G+ 
Sbjct: 255 LLEVRNISDGKRF------HDIHFNLRPGEILGIGGLMGAGRSEIAQGICALQPLTRGSI 308

Query: 63  ELDGKP-----YSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAV 117
            + G+P     Y+ S    +      R  ++  LF  M +  N+     +R   +  G  
Sbjct: 309 RIKGEPVRLKDYAASIQQRMVYLSEDR--KDAGLFLAMPIDWNISA-LDIRAVSH-HGLT 364

Query: 118 FRHKAAREEEAAIRE----KSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQ 173
              +  R +  A+ +    K  KL D V            LS G+Q+++ +AR L+  P+
Sbjct: 365 LSPRRERLQAEALAQQVKLKRGKLSDPVS----------SLSGGNQQKVALARVLSVQPE 414

Query: 174 LLALDEPAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGK 230
           ++ LDEP  G++ + K  + ++L  +   G  +++I  ++  ++GLC+RI V+  G+
Sbjct: 415 IVFLDEPTRGVDVSAKAEIYQILANLAGNGVGLVVISSELPELIGLCDRIIVIHEGR 471


Lambda     K      H
   0.320    0.138    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 300
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 500
Length adjustment: 29
Effective length of query: 226
Effective length of database: 471
Effective search space:   106446
Effective search space used:   106446
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory